Consulting

Configuration

Compute Nodes

The Genepool system is made up of a heterogeneous collection of nodes to serve the diverse workload of the JGI users. Below is a table of the current configuration.

# Nodes

Cores/node

Memory/node

Local disk

Processor

Hostname

Vendor

2

32

1000GB

3.6TB

Xeon E5-4650L

mndlhm0205-ib,mndlhm0405-ib.nersc.gov

Appro/Cray

5

32

500GB

3.6TB

Xeon E5-4650L

mndlhm[01-05]03.nersc.gov

Appro/Cray

8

16

248GB

1.8TB

Xeon E5-2670

mc0xxx.nersc.gov

Appro/Cray

212

16

120GB

1.8TB

Xeon E5-2670

mc0xxx.nersc.gov

Appro/Cray

450

8

48 GB

1 TB

Intel Xeon L5520 2.27 GHz

sgi[01a01-06b40].nersc.gov

SGI

64

8

48 GB

500 GB

Intel Xeon L5520 2.27 GHz

quad[01-64].nersc.gov

SuperMicro

20

8

144 GB

512 GB

Intel Xeon L5520 2.27 GHz

x4170a[01-20].nersc.gov

Sun

4

32

512 GB

1 TB

AMD Opteron 2.28 GHz

gpht-[01-04].nersc.gov

Sun

1

80

2 TB

300 GB

Intel Xeon X7560 2.27 GHz

b2r2ibm1t-02.nersc.gov

IBM

1

32

1 TB

600 GB

Intel Xeon X7560 2.27 GHz

gptb-01.nersc.gov

Dell

7

24

256 GB

600 GB

Intel x7542 2.67 GHz

uv10-[1-7].nersc.gov

SGI

Login Nodes

Genepool currently has four login nodes. Users land on one of the four login nodes when they ssh to genepool.nersc.gov. The different login nodes sit behind a load balancer and youyou will land on the login node with the least number of connections, or if you already have active connections, you will be directed to the same login node. The names of the login nodes are genepool01, genepool02, genepool03 and genepool04, however you should always access the login nodes with ssh username@genepool.nersc.gov. The login nodes have 32 GB of RAM, have 2.3GHz processors and have 8 cores each.

"gpint" Analysis Nodes

Genepool also has nodes which are used for pipeline control and pre- and post-processing of jobs as well as analysis jobs. At present, these nodes are allocated per group and are called gpintNN (NN = 01,02,...). Users should refer to the table below to determine which node belongs to their group and only use the nodes allocated to their group. Note: the legacy gpints (01-27) will be retired in the coming weeks. gpint05, gpint11, and gpint13 will remain in service. Higher numbered gpints (100+) are replacing the legacy nodes.

Node Name

Legacy JGI Name

Assigned Group

Cores

Memory

Per-process

Memory Limit

gpint01.nersc.gov

one.jgi-psf.org

R & D

24

252.4 GB

214.56 GB

gpint02.nersc.gov

bcg1.jgi-psf.org

Comparative Genomics (Vista)

16

31.5 GB

N/A

gpint03.nersc.gov

bcg2.jgi-psf.org

Comparative Genomics (Vista)

16

31.5 GB

N/A

gpint04.nersc.gov

merced.jgi-psf.org

IMG

16

63.0 GB

53.59 GB

gpint05.nersc.gov

img-worker.jgi-psf.org

IMG

32

505 GB

429.23 GB

gpint06.nersc.gov

zeus.jgi-psf.org

GBP

16

63.0 GB

53.59 GB

gpint07.nersc.gov

ranger.jgi-psf.org

Plant

24

252.4 GB

214.56 GB

gpint08.nersc.gov

boiler.jgi-psf.org

Plant

24

252.4 GB

214.56 GB

gpint09.nersc.gov

sedona.jgi-psf.org

Plant

24

252.4 GB

214.56 GB

gpint10.nersc.gov

willow.jgi-psf.org

Plant

24

252.4 GB

214.56 GB

gpint11.nersc.gov

actinium.jgi-psf.org

Plant

32

505 GB

429.23 GB

gpint12.nersc.gov

bat.jgi-psf.org

R & D

24

239.9 GB

203.91 GB

gpint13.nersc.gov

quarter.jgi-psf.org

Fungal

48

252.4 GB

214.54 GB

gpint14.nersc.gov

chekov.jgi-psf.org

General purpose

16

63GB

52.9GB

gpint15.nersc.gov

stimpy.jgi-psf.org

General purpose

8

47.3 GB

40.17 GB

gpint16.nersc.gov

ren.jgi-psf.org

General purpose

8

62.3 GB

52.91 GB

gpint17.nersc.gov

thallium.jgi-psf.org

General purpose

16

108.4 GB

92.16 GB

gpint18.nersc.gov

indium.jgi-psf.org

General purpose

16

126.2 GB

107.24 GB

gpint19.nersc.gov

gallium.jgi-psf.org

General purpose

16

126.2 GB

107.24 GB

gpint20.nersc.gov

cadmium.jgi-psf.org

General purpose

16

126.2 GB

107.24 GB

gpint21.nersc.gov

itchy.jgi-psf.org

General purpose

16

165.7 GB

140.83 GB

gpint22.nersc.gov

wesley.jgi-psf.org

General purpose

16

70.9 GB

60.29 GB

gpint23.nersc.gov

n/a

SDM - PacBio

8

47.3 GB

40.17 GB

gpint24.nersc.gov

rqc-dev.jgi-psf.org

RQC

8

47.3 GB

40.17 GB

gpint25.nersc.gov

rqc-prod.jgi-psf.org

RQC

8

47.3 GB

40.17 GB

gpint26.nersc.gov

sdm-dev.jgi-psf.org

SDM

8

47.3 GB

40.17 GB

gpint27.nersc.gov

sdm-prod.jgi-psf.org

SDM

8

47.3 GB

40.17 GB

gpint100.nersc.gov

R & D

16

256G

208G

gpint101.nersc.gov

R & D

16

256G

208G

gpint102.nersc.gov

Plant

16

256G

208G

gpint103.nersc.gov

Plant

16

256G

208G

gpint104.nersc.gov

Plant

16

128G

101G

gpint105.nersc.gov

IMG

16

128G

101G

gpint106.nersc.gov

GBP

16

128G

101G

gpint107.nersc.gov

SDM

16

128G

101G

gpint108.nersc.gov

RQC

16

128G

101G

gpint109.nersc.gov

Assembly

16

128G

101G

gpint110.nersc.gov

Assembly

16

128G

101G

gpint111.nersc.gov

Vista

16

128G

101G

gpint112.nersc.gov

Common

16

128G

101G

Other Special Purpose Nodes

Nodes which perform specialized tasks such as running a web-server and/or databases are also part of Genepool, although they may not have all the features of login or analysis nodes (such as NGF filesystems, login access, etc.). These nodes are also currently assigned on a per-group basis. Use of these nodes is restricted to the groups to which they have been assigned.